One extensively investigated form of perceptual bistability is binocular rivalry—When dissimilar patterns are presented one to each eye, these patterns compete for perceptual dominance. Here, we report that transcranial magnetic stimulation (TMS) over early visual areas induces alternations during binocular rivalry. The effect of TMS on binocular rivalry was retinotopic, suggesting that rivalry mechanisms are localized in the cortical representation of visual space. The timing of perturbations was highly dependent on individual differences in rivalry alternation frequencies, with more delayed effects found in slower alternators. This finding suggests that both binocular rivalry and TMS dynamics might be contingent on individual differences among observers. We performed an analogous set of experiments by replacing TMS with transient visual stimulation. The results, however, qualitatively and quantitatively differed from those reported with TMS. Finally, we found that TMS over early visual areas does not produce any time-locked effects on another dynamical process—eye-swapping stimulus rivalry. These findings constitute the first causative evidence that binocular rivalry is contingent on neural activity in early visual areas and suggest that binocular rivalry and stimulus rivalry have different neural correlates, supporting multilevel theories of visual rivalry.